use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils qw(clone_Transcript);
or
use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils
to get all methods

Description

All methods in this class should take a Bio::EnsEMBL::Transcriptobject as their first argument.The methods provided should carry out some standard functionality for said objects such as printing info, and cloning and checking phase consistency or splice sites etc

Arg [1] : Bio::EnsEMBL::Transcript Function : to check that end phase of one exon is always the same as start phase of the next. The only acceptable exception to this is an end phase of -1 and a start phase of 0/1/2 or vice versa as UTR exons always have end phase of -1 but the whole of the next exon may be coding and to give it a start phase of -1 is considered misleading Returntype: boolean, 1 for pass 0 for fail (ie phase inconsistency) Exceptions: none Example :

Arg [1] : Bio::EnsEMBL::Transcript Function : produce a new copy of the transcript object passed in so it can be altered without impact on the original objects the only bit it doesnt keep is the adaptor so the cloned object can be stored Returntype: Bio::EnsEMBL::Transcript Exceptions: none Example : my $newtranscript = clone_Transcript($transcript);

Arg [1] : Bio::EnsEMBL::Transcript Arg [2] : hashref, a hash of ids which are unwanted Function : To ensure the given transcript is not supported by any of the unwanted evidence Returntype: boolean, 1 for no unwanted evidence, 0 for unwanted evidence Exceptions: Example :

Title : identical_Transcripts Usage : $identical = identical_Transcripts($transcript1, $transcript2); Function: compares 2 Transcripts. DOES NOT CHECK TO SEE WHETHER PHASES ARE IDENTICAL OR WHETHER EVIDENCE IS IDENTICAL. Transcripts are compared on the basis of (i) number of Exons, (ii) start and end coordinates for each Transcript, (iii) strand Example : Returns : 1 if identical, 0 if not indentical Args : Transcript, Transcript

Arg [1] : Bio::EnsEMBL::Transcript or Aref of Bio::EnsEMBL::Transcript-objects Arg [2] : string, this should be a string or spaces or tabs to indent the printed string
Function : print information about the transcript and its
children objects, using indent to make the format readable
Returntype: n/a
Exceptions: none
Example : print_Transcript($transcript);

Arg [1] : Bio::EnsEMBL::Transcript or Aref of Bio::EnsEMBL::Transcript-objects Arg [2] : string, this should be a string or spaces or tabs to indent the printed string
Function : print information about the transcript and its Exons
using indent to make the format readable
Returntype: n/a
Exceptions: none
Examples : print_Transcript_and_Exons(\@transcript)
print_Transcript_and_Exons($transcript)

Arg [1] : arrayref Bio::EnsEMBL::Transcript Arg [2] : Bio::EnsEMBL::Transcript Function : Intended to be called after split_Transcripts Performs a series of standard gene-buildy checks on the given transcripts, Args : The original transcripts, and the results of split_Transcript Returns : arrayref of transcripts that pass checks

Arg [1] : Bio::EnsEMBL::Transcript Function : when start/end of translation is flush to start/end of transcript, and phase is non-zero, trim back to whole codon. If we have UTR adjacent to a non-zero phase codon, then something is wrong, so best to leave it alone Returntype: Bio::EnsEMBL::Transcript Exceptions: Example :